Scalpel

Introduction

Scalpel is a software package for detecting INDELs (INsertions and DELetions) mutations in
a reference genome which has been sequenced with next-generation sequencing technology
(e.g., Illumina).
Scalpel is designed to perform localized micro-assembly of specific regions of interest
with the goal of detecting mutations with high accuracy and increased power.
It is based on the de Bruijn graph assembly paradigm and implements an
on-the-fly repeat composition analysis coupled with a self-tuning k-mer strategy to
increase specificity in regions characterized by complex repeat structures.
It supports three different modes of operation:

Single: in single mode scalpel detects INDELs in one single dataset (e.g., one individual exome).

Denovo: in denovo mode scalpel detects de novo INDELs in one family of four individuals (mom, dad, aff, sib).